package org.proteored.miapeapi.cv.msi;

import org.proteored.miapeapi.cv.Accession;
import org.proteored.miapeapi.cv.ControlVocabularyManager;
import org.proteored.miapeapi.cv.ControlVocabularySet;

public class AdditionalParameterName extends ControlVocabularySet {
	/*
	 * SEARCH_ENGINE_SPECIFIC_INPUT_PARAMETER("MS:1001302",
	 * "search engine specific input parameter"),
	 * SEQUEST_SORT_BY_RSP("MS:1001059", "sequest:sort_by_RSp"),
	 * PROTEINEXTRACTOR_USEPHENYX("MS:1001443", "ProteinExtractor:UsePhenyx"),
	 * PROTEINEXTRACTOR_PROTEINSOLVERWEIGHTING("MS:1001442",
	 * "ProteinExtractor:ProteinSolverWeighting"),
	 * PROTEINEXTRACTOR_PROTEINSOLVERUNIQUESCORE("MS:1001441",
	 * "ProteinExtractor:ProteinSolverUniqueScore"),
	 * PROTEINEXTRACTOR_PROTEINSOLVERPEPTIDESCORETHRESHOLD("MS:1001440",
	 * "ProteinExtractor:ProteinSolverPeptideScoreThreshold"),
	 * PROTEINEXTRACTOR_USESEQUEST("MS:1001435", "ProteinExtractor:UseSequest"),
	 * PROTEINEXTRACTOR_SEQUESTPEPTIDESCORETHRESHOLD("MS:1001436",
	 * "ProteinExtractor:SequestPeptideScoreThreshold"),
	 * PROTEINEXTRACTOR_MASCOTUSEIDENTITYSCORE("MS:1001433",
	 * "ProteinExtractor:MascotUseIdentityScore"),
	 * PROTEINEXTRACTOR_MASCOTWEIGHTING("MS:1001434",
	 * "ProteinExtractor:MascotWeighting"),
	 * PROTEINEXTRACTOR_USEPROTEINSOLVER("MS:1001439",
	 * "ProteinExtractor:UseProteinSolver"),
	 * PROTEINEXTRACTOR_SEQUESTUNIQUESCORE("MS:1001437",
	 * "ProteinExtractor:SequestUniqueScore"),
	 * PROTEINEXTRACTOR_SEQUESTWEIGHTING("MS:1001438",
	 * "ProteinExtractor:SequestWeighting"), SEQUEST_SORT_BY_TIC("MS:1001069",
	 * "sequest:sort_by_TIC"), SEQUEST_SORT_BY_SP("MS:1001068",
	 * "sequest:sort_by_Sp"), SEQUEST_PROCESSALL("MS:1001095",
	 * "sequest:ProcessAll"), SEQUEST_TOPPERCENTMOSTINTENSE("MS:1001096",
	 * "sequest:TopPercentMostIntense"), SEQUEST_SORT_BY_IONS("MS:1001048",
	 * "sequest:sort_by_Ions"), SEQUEST_SORT_BY_MH("MS:1001049",
	 * "sequest:sort_by_MH+"), MASCOT_INCLUDEERRORTOLERANTMATCHES("MS:1001324",
	 * "mascot:IncludeErrorTolerantMatches"),
	 * MASCOT_USEUNIGENECLUSTERING("MS:1001323", "mascot:UseUnigeneClustering"),
	 * MASCOT_SHOWDECOYMATCHES("MS:1001325", "mascot:ShowDecoyMatches"),
	 * SEQUEST_OUTPUTLINES("MS:1001007", "sequest:OutputLines"),
	 * SEQUEST_CHROMATOGRAM("MS:1001102", "sequest:Chromatogram"),
	 * SEQUEST_VIEWCV("MS:1001006", "sequest:ViewCV"),
	 * SEQUEST_CLEAVESAT("MS:1001005", "sequest:CleavesAt"),
	 * PROTEINEXTRACTOR_USEMASCOT("MS:1001430", "ProteinExtractor:UseMascot"),
	 * PROTEINEXTRACTOR_MASCOTUNIQUESCORE("MS:1001432",
	 * "ProteinExtractor:MascotUniqueScore"),
	 * SEQUEST_DESCRIPTIONLINES("MS:1001009", "sequest:DescriptionLines"),
	 * PROTEINEXTRACTOR_MASCOTPEPTIDESCORETHRESHOLD("MS:1001431",
	 * "ProteinExtractor:MascotPeptideScoreThreshold"),
	 * SEQUEST_SORT_BY_Z("MS:1001094", "sequest:sort_by_z"),
	 * PROTEINEXTRACTOR_METHODNAME("MS:1001424", "ProteinExtractor:Methodname"),
	 * PROTEINEXTRACTOR_GENERATENONREDUNDANT("MS:1001425",
	 * "ProteinExtractor:GenerateNonRedundant"),
	 * PROTEINEXTRACTOR_INCLUDEIDENTIFIED("MS:1001426",
	 * "ProteinExtractor:IncludeIdentified"), SEQUEST_SORT_BY_P("MS:1001050",
	 * "sequest:sort_by_P"), PROTEINEXTRACTOR_MAXNUMBEROFPROTEINS("MS:1001427",
	 * "ProteinExtractor:MaxNumberOfProteins"),
	 * PROTEINEXTRACTOR_MAXPROTEINMASS("MS:1001428",
	 * "ProteinExtractor:MaxProteinMass"),
	 * PROTEINEXTRACTOR_MINNUMBEROFPEPTIDES("MS:1001429",
	 * "ProteinExtractor:MinNumberOfPeptides"),
	 * SEQUEST_SORT_BY_REF("MS:1001053", "sequest:sort_by_Ref"),
	 * SEQUEST_SORT_BY_PREVIOUSAMINOACID("MS:1001052",
	 * "sequest:sort_by_PreviousAminoAcid"), SEQUEST_CONSENSUS("MS:1001038",
	 * "sequest:Consensus"), SEQUEST_FULL("MS:1001111", "sequest:Full"),
	 * MASCOT_PROTEINSCORINGMETHOD("MS:1001318", "mascot:ProteinScoringMethod"),
	 * SEQUEST_SHOWFRAGMENTIONS("MS:1001037", "sequest:ShowFragmentIons"),
	 * SEQUEST_MODECV("MS:1001110", "sequest:modeCV"),
	 * MASCOT_MINMSMSTHRESHOLD("MS:1001319", "mascot:MinMSMSThreshold"),
	 * MASCOT_SIGTHRESHOLD("MS:1001316", "mascot:SigThreshold"),
	 * MASCOT_MAXPROTEINHITS("MS:1001317", "mascot:MaxProteinHits"),
	 * SEQUEST_INFOANDLOG("MS:1001103", "sequest:InfoAndLog"),
	 * SEQUEST_SELECTCV("MS:1001128", "sequest:selectCV"),
	 * SEQUEST_SORT_BY_DCN("MS:1001046", "sequest:sort_by_dCn"),
	 * SEQUEST_SORT_BY_DM("MS:1001047", "sequest:sort_by_dM"),
	 * SEQUEST_TOPNUMBER("MS:1001106", "sequest:TopNumber"),
	 * SEQUEST_FAST("MS:1001126", "sequest:Fast"),
	 * MASCOT_REQUIREBOLDRED("MS:1001322", "mascot:RequireBoldRed"),
	 * SEQUEST_SORTCV("MS:1001041", "sequest:sortCV"),
	 * MASCOT_SHOWHOMOLOGOUSPROTEINSWITHSUBSETOFPEPTIDES("MS:1001321",
	 * "mascot:ShowHomologousProteinsWithSubsetOfPeptides"),
	 * SEQUEST_LIMITTO("MS:1001042", "sequest:LimitTo"),
	 * SEQUEST_CULLTO("MS:1001109", "sequest:CullTo"),
	 * MASCOT_SHOWHOMOLOGOUSPROTEINSWITHSAMEPEPTIDES("MS:1001320",
	 * "mascot:ShowHomologousProteinsWithSamePeptides"),
	 * PHENYX_DEFAULT_PARENT_CHARGE("MS:1001377",
	 * "Phenyx:Default Parent Charge"), PHENYX_SCORING_MODEL("MS:1001376",
	 * "Phenyx:Scoring Model"), PHENYX_INSTRUMENT_TYPE("MS:1001375",
	 * "Phenyx:Instrument Type"), SEQUEST_PROCESSCV("MS:1001087",
	 * "sequest:ProcessCV"), SEQUEST_SORT_BY_XCORR("MS:1001086",
	 * "sequest:sort_by_XCorr"), PHENYX_TRUST_PARENT_CHARGE("MS:1001378",
	 * "Phenyx:Trust Parent Charge"), PHENYX_TURBO("MS:1001379",
	 * "Phenyx:Turbo"), SEQUEST_FORMATANDLINKS("MS:1001120",
	 * "sequest:FormatAndLinks"), SEQUEST_SELECTDEFAULT("MS:1001144",
	 * "sequest:SelectDefault"), SEQUEST_SEQUENCEHEADERFILTER("MS:1001028",
	 * "sequest:SequenceHeaderFilter"),
	 * SEQUEST_NORMALIZEXCORRVALUES("MS:1001026",
	 * "sequest:NormalizeXCorrValues"),
	 * TODOSEQUEST_SELECTADVANCEDCV("MS:1001145",
	 * "TODOsequest:SelectAdvancedCV"), SEQUEST_SORT_BY_SF("MS:1001072",
	 * "sequest:sort_by_Sf"), SEQUEST_SORT_BY_SEQUENCE("MS:1001071",
	 * "sequest:sort_by_Sequence"), SEQUEST_SORT_BY_SCAN("MS:1001070",
	 * "sequest:sort_by_Scan"), SEQUEST_SEQUENCEPARTIALFILTER("MS:1001032",
	 * "sequest:SequencePartialFilter"), PHENYX_TURBO_ERRORTOL("MS:1001380",
	 * "Phenyx:Turbo:ErrorTol"), OMSSA_E_VALUE_THRESHOLD("MS:1001449",
	 * "OMSSA e-value threshold"), PHENYX_TURBO_SERIES("MS:1001382",
	 * "Phenyx:Turbo:Series"), PHENYX_TURBO_COVERAGE("MS:1001381",
	 * "Phenyx:Turbo:Coverage"), PHENYX_MINPEPZSCORE("MS:1001384",
	 * "Phenyx:MinPepzscore"), PHENYX_MINPEPLENGTH("MS:1001383",
	 * "Phenyx:MinPepLength"), PROTEINEXTRACTOR_PHENYXUNIQUESCORE("MS:1001445",
	 * "ProteinExtractor:PhenyxUniqueScore"), PHENYX_AC_SCORE("MS:1001386",
	 * "Phenyx:AC Score"),
	 * PROTEINEXTRACTOR_PHENYXPEPTIDESCORETHRESHOLD("MS:1001444",
	 * "ProteinExtractor:PhenyxPeptideScoreThreshold"),
	 * PHENYX_MAXPEPPVALUE("MS:1001385", "Phenyx:MaxPepPvalue"),
	 * PROTEINEXTRACTOR_PHENYXWEIGHTING("MS:1001446",
	 * "ProteinExtractor:PhenyxWeighting"),
	 * PHENYX_CONFLICT_RESOLUTION("MS:1001387", "Phenyx:Conflict Resolution"),
	 * MINIMUM_NUMBER_OF_ENZYMATIC_TERMINI("MS:1001578",
	 * "Minimum Number of Enzymatic Termini"),
	 * SCAFFOLD__MINIMUM_PEPTIDE_PROBABILITY("MS:1001577",
	 * "Scaffold: Minimum Peptide Probability"),
	 * SCAFFOLD__MINIMUM_PROTEIN_PROBABILITY("MS:1001576",
	 * "Scaffold: Minimum Protein Probability"),
	 * SCAFFOLD__MINIMUM_PEPTIDE_COUNT("MS:1001575",
	 * "Scaffold: Minimum Peptide Count"),
	 * IONS_SERIES_CONSIDERED_IN_SEARCH("MS:1001066",
	 * "ions series considered in search"), PARAM__X_ION("MS:1001261",
	 * "param: x ion"), PARAM__W_ION("MS:1001260", "param: w ion"),
	 * PARAM__Z_ION("MS:1001263", "param: z ion"), PARAM__Y_ION("MS:1001262",
	 * "param: y ion"), PARAM__Y_ION_H2O("MS:1001152", "param: y ion-H2O"),
	 * PARAM__A_ION_NH3("MS:1001146", "param: a ion-NH3"),
	 * PARAM__Y_ION_NH3("MS:1001151", "param: y ion-NH3"),
	 * PARAM__B_ION_H2O("MS:1001150", "param: b ion-H2O"),
	 * PARAM__INTERNAL_YB_ION("MS:1001406", "param: internal yb ion"),
	 * PARAM__INTERNAL_YA_ION("MS:1001407", "param: internal ya ion"),
	 * PARAM__B_ION_NH3("MS:1001149", "param: b ion-NH3"),
	 * PARAM__A_ION("MS:1001108", "param: a ion"), PARAM__B_ION("MS:1001118",
	 * "param: b ion"), PARAM__C_ION("MS:1001119", "param: c ion"),
	 * PARAM__A_ION_H2O("MS:1001148", "param: a ion-H2O"),
	 * PARAM__V_ION("MS:1001257", "param: v ion"), PARAM__D_ION("MS:1001258",
	 * "param: d ion"), PARAM__IMMONIUM_ION("MS:1001259",
	 * "param: immonium ion"), PARAM__Z_1_ION("MS:1001408", "param: z+1 ion"),
	 * PARAM__Z_2_ION("MS:1001409", "param: z+2 ion");
	 */

	public static final Accession PHENYX_SCORING_MODEL = new Accession("MS:1001376");
	public static final Accession SEARCH_ENGINE_INPUT_PARAMETER = new Accession("MS:1002093");
	public static final Accession ION_SERIES_CONSIDERED_IN_THE_SEARCH = new Accession("MS:1001066");
	private static AdditionalParameterName instance;

	public static AdditionalParameterName getInstance(ControlVocabularyManager cvManager) {
		if (instance == null)
			instance = new AdditionalParameterName(cvManager);
		return instance;
	}

	private AdditionalParameterName(ControlVocabularyManager cvManager) {
		super(cvManager);

		String[] parentAccessionsTMP = { SEARCH_ENGINE_INPUT_PARAMETER.toString(),
				ION_SERIES_CONSIDERED_IN_THE_SEARCH.toString() };
		this.parentAccessions = parentAccessionsTMP;

		this.miapeSection = 305;

	}

}